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- PDB-1q65: CRYSTAL STRUCTURE OF TGT IN COMPLEX WITH 2,6-DIAMINO-8-(2-dimethy... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1q65 | ||||||
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Title | CRYSTAL STRUCTURE OF TGT IN COMPLEX WITH 2,6-DIAMINO-8-(2-dimethylaminoethylsulfanylmethyl)-3H-QUINAZOLIN-4-ONE crystallized at pH 5.5 | ||||||
![]() | Queuine tRNA-ribosyltransferase | ||||||
![]() | TRANSFERASE | ||||||
Function / homology | ![]() tRNA-guanosine34 preQ1 transglycosylase / tRNA wobble guanine modification / tRNA-guanosine(34) queuine transglycosylase activity / tRNA-guanine transglycosylation / queuosine biosynthetic process / metal ion binding / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Brenk, R. / Meyer, E. / Reuter, K. / Stubbs, M.T. / Garcia, G.A. / Klebe, G. | ||||||
![]() | ![]() Title: Crystallographic Study of Inhibitors of tRNA-guanine Transglycosylase Suggests a New Structure-based Pharmacophore for Virtual Screening. Authors: Brenk, R. / Meyer, E. / Reuter, K. / Stubbs, M.T. / Garcia, G.A. / Diederich, F. / Klebe, G. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 91.9 KB | Display | ![]() |
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PDB format | ![]() | 67.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 685.9 KB | Display | ![]() |
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Full document | ![]() | 694.5 KB | Display | |
Data in XML | ![]() | 18.7 KB | Display | |
Data in CIF | ![]() | 26.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1q4wC ![]() 1q63C ![]() 1q66C ![]() 1r5yC ![]() 1pudS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 42925.703 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: P28720, tRNA-guanosine34 preQ1 transglycosylase |
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#2: Chemical | ChemComp-ZN / |
#3: Chemical | ChemComp-BHB / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.42 Å3/Da / Density % sol: 49.2 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: PEG 8000, TRIS, DMSO, DTT, pH 5.50, VAPOR DIFFUSION, HANGING DROP, temperature 295K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jul 28, 1999 / Details: MIRRORS |
Radiation | Monochromator: YALE MIRROR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→40 Å / Num. obs: 24075 / % possible obs: 100 % / Redundancy: 3.7 % / Biso Wilson estimate: 15.7 Å2 / Rsym value: 0.074 |
Reflection shell | Resolution: 2.1→2.26 Å / Rsym value: 0.291 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1PUD Resolution: 2.1→40 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 398796.95 / Data cutoff high rms absF: 398796.95 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 60.3623 Å2 / ksol: 0.334042 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 27.5 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.1→40 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.1→2.23 Å / Rfactor Rfree error: 0.015 / Total num. of bins used: 6
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Xplor file |
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